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I think the Geonosians designed and were going to build the Death Star, until the Republic showed up. I get the sense they were exterminated to keep a secret.
There were rumors that this Jyn character is the son of the guy in charge of building the Death Star. It would make sense that he would be a high ranking officer, as the rank insignia suggests.
My question is, why is he holding that big blaster on what appears to be the bridge of the Death Star?
Yes, I believe that is what has been implied and I also think that stems from the old EU/now Legends material. I don't believe it has been made canon why they were exterminated. My guess is that I'd look for that to be made canon in the next season of Rebels via Kallus looking into the atrocities of the Empire. If you have watched Rebels, I think they've setup him to start doubting the Empire's intentions as of "The Honorable Ones" from this season.
Ah, I see you have either read MSW or some other place where rumors have been posted. I've read that too (well daughter, not son), and think it would make for an interesting story. Edwards has said that this film more of a world of shades of grey and not dark vs light like the trilogy films are. It's pretty clear that Jyn Erso has no love for the Empire based on the trailer given her criminal history that is mentioned. Also on the shades of grey thing, I think some of the characters we have seen in the trailer (I'm thinking of Whitaker's character specifically) have switched from their former allegiance.
In regards to Mendelsohn's character, it screams Imperial Security Bureau. Remember Wullf Yularen from ANH? Similar uniform, though Yularen was obviously lower in rank in ANH. I personally think (and this is from me, not read anywhere else) that he is standing there preparing to execute one of the rebel spies. The problem is that besides Yularen, Kallus is the only example we have in canon that is from the ISB and his uniform looks nothing like Mendelsohn's.
Edit: Apparently the extermination was made canon in the Darth Vader comics.